Atomistic simulation together with micromechanical analysis was employed to characterize the Young’s modulus and thermal conductivity of graphene/epoxy nanocomposites. Nanocomposites containing pristine graphene, carboxyl (COOH)-functionalized graphene, and COOH- and amine (NH₂)-functionalized graphene were considered in the simulations. The effect of atomistic interaction between the graphene and the surrounding epoxy was accounted for in the molecular dynamics simulations and then used to derive the effective properties of graphene. Subsequently, the Young’s modulus and thermal conductivity of nanocomposites containing randomly oriented graphene were modeled using the Mori–Tanaka micromechanical model. The results indicated that the COOH- and NH₂-functionalized graphene nanocomposite had superior mechanical and thermal properties to the other two material systems. Moreover, the model predictions were in favorable agreement with the experimental data.